Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

Abstract

The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids

“…The successful control of viruses and viroids in commercial crops are directedly correlated to the effectiveness of the detection assays used to screen plant propagation material. The challenges and opportunities of HTS for virus and viroid detection has been highlighted previously [ 14 – 17 ] and in the United States of America, HTS already forms part of their clean plant propagation programs by creating a provisional release category based on a HTS-negative selection [ 16 ]. This category of plants is then allowed to be propagated in designated approved areas pending the completion of all conventional laboratory tests.…”

From boots on the ground to nucleotides in the sequencer: a century of advances in the study of the plant virus ecology

“…Les évaluations individuelles examinent des individus choisis aléatoirement sur le terrain, tandis que les évaluations basées sur un échantillon évaluent le nombre de taxons cibles dans des unités d'échantillonnage collectives telles que les quadrats [105]. Le choix entre ces modalités peut de façon évidente impacter les valeurs de richesse et de diversité virales, ou la capacité à reconstituer ou non des molécules génomiques complètes [106].…”

Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses

“…Recent advances in metagenomics applied to viruses has fostered a greater inventory of the viral diversity [ 1 , 2 , 3 , 4 ]. Hence, the large scale sampling of oceanic water [ 5 , 6 ], plants, animals, and humans [ 7 , 8 , 9 , 10 ], extreme environments [ 11 ], or the mining of genomic and transcritptomic data [ 12 , 13 , 14 , 15 ] have completely shifted our understanding of viral diversity and the function of viruses in host populations or even at the global ecosystem scale. However, these inventories remain largely incomplete, and the current knowledge of the virus diversity probably only represents the contour of the extant diversity [ 4 ].…”